diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 32 |
1 files changed, 21 insertions, 11 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 285b01d..50c207d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1609,7 +1609,8 @@ runApp(launch.browser=0, port=4208)~%\n" (file-name (git-file-name name version)) (sha256 (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) - (patches (search-patches "seqwish-paryfor-riscv.diff")) + (patches (search-patches "seqwish-paryfor-riscv.diff" + "seqwish-shared-library.diff")) (snippet #~(begin (use-modules (guix build utils)) @@ -1626,14 +1627,24 @@ runApp(launch.browser=0, port=4208)~%\n" (build-system cmake-build-system) (arguments `(#:configure-flags - '(,@(if (target-x86?) - ;; This is the minimum needed to compile on x86_64, and is a - ;; subset of any other optimizations which might be applied. - '("-DCMAKE_C_FLAGS=-mcx16" - "-DCMAKE_CXX_FLAGS=-mcx16") - '())) + (cons* ,@(if (target-x86?) + ;; This is the minimum needed to compile on x86_64, and is a + ;; subset of any other optimizations which might be applied. + '("-DCMAKE_C_FLAGS=-mcx16" + "-DCMAKE_CXX_FLAGS=-mcx16") + '()) + '("-DSEQWISH_LINK_SHARED_LIBRARY=ON")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; This stashes the build version in the executable. + (mkdir "include") + (substitute* "CMakeLists.txt" + (("^execute_process") "#execute_process")) + (with-output-to-file "include/seqwish_git_version.hpp" + (lambda () + (format #t "#define SEQWISH_GIT_VERSION \"~a\"~%" ,version))))) (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("CMakeLists.txt" @@ -1642,11 +1653,10 @@ runApp(launch.browser=0, port=4208)~%\n" (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") (("\\$\\{sdsl-lite_INCLUDE\\}") - (string-append (assoc-ref inputs "sdsl-lite") - "/include/sdsl")) + (search-input-directory inputs "/include/sdsl")) (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") - (string-append (assoc-ref inputs "libdivsufsort") - "/include"))))) + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. |